ADIOS2 issueshttps://code.ornl.gov/pnb/ADIOS2/-/issues2019-10-04T03:27:14Zhttps://code.ornl.gov/pnb/ADIOS2/-/issues/1804Build Error in ADIOS 2.5.0 on OSX: JsonWorker2019-10-04T03:27:14ZPodhorszki, NorbertBuild Error in ADIOS 2.5.0 on OSX: JsonWorker*Created by: ax3l*
Reference: https://dev.azure.com/conda-forge/feedstock-builds/_build/results?buildId=76704 in https://github.com/conda-forge/adios2-feedstock/pull/8
Compiler: Clang 4.0.1 on Apple-Darwin13.4.0
CMake feature matr...*Created by: ax3l*
Reference: https://dev.azure.com/conda-forge/feedstock-builds/_build/results?buildId=76704 in https://github.com/conda-forge/adios2-feedstock/pull/8
Compiler: Clang 4.0.1 on Apple-Darwin13.4.0
CMake feature matrix:
```
ADIOS2 build configuration:
ADIOS Version: 2.5.0
C++ Compiler : Clang 4.0.1
/usr/local/miniconda/conda-bld/adios2_1569893413423/_build_env/bin/x86_64-apple-darwin13.4.0-clang++
Installation prefix: /usr/local/miniconda/conda-bld/adios2_1569893413423/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh
bin: bin
lib: lib
include: include
cmake: lib/cmake/adios2
python: lib/python3.6/site-packages
Features:
Library Type: shared
Build Type: Release
Testing: OFF
Examples: OFF
Build Options:
Blosc : ON
BZip2 : OFF
ZFP : OFF
SZ : OFF
MGARD : OFF
PNG : ON
MPI : ON
DataMan : ON
Table : ON
SSC : ON
SST : ON
DataSpaces: OFF
ZeroMQ : ON
HDF5 : ON
Python : ON
Fortran : OFF
SysVShMem: ON
Profiling: ON
Endian_Reverse: OFF
RDMA Transport for Staging: Unconfigured
```
Compile error:
```
/usr/local/miniconda/conda-bld/adios2_1569893413423/work/source/adios2/toolkit/query/JsonWorker.cpp:128:37: error: call to member function 'compare' is ambiguous
if (m_SourceReader->m_IO.m_Name.compare(ioName) != 0)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~
/usr/local/miniconda/conda-bld/adios2_1569893413423/_build_env/bin/../include/c++/v1/string:1189:9: note: candidate function
int compare(const basic_string& __str) const _NOEXCEPT;
^
/usr/local/miniconda/conda-bld/adios2_1569893413423/_build_env/bin/../include/c++/v1/string:1191:9: note: candidate function
int compare(__self_view __sv) const _NOEXCEPT;
^
/usr/local/miniconda/conda-bld/adios2_1569893413423/_build_env/bin/../include/c++/v1/string:1205:9: note: candidate function not viable: no known conversion from 'nlohmann::basic_json<std::map, std::vector, std::__1::basic_string<char>, bool, long long, unsigned long long, double, std::allocator, adl_serializer>' to 'const value_type *' (aka 'const char *') for 1st argument
int compare(const value_type* __s) const _NOEXCEPT;
^
/usr/local/miniconda/conda-bld/adios2_1569893413423/_build_env/bin/../include/c++/v1/string:1204:9: note: candidate function template not viable: requires at least 4 arguments, but 1 was provided
compare(size_type __pos1, size_type __n1, const _Tp& __t, size_type __pos2, size_type __n2=npos) const;
^
/usr/local/miniconda/conda-bld/adios2_1569893413423/_build_env/bin/../include/c++/v1/string:1193:9: note: candidate function not viable: requires 3 arguments, but 1 was provided
int compare(size_type __pos1, size_type __n1, __self_view __sv) const;
^
/usr/local/miniconda/conda-bld/adios2_1569893413423/_build_env/bin/../include/c++/v1/string:1195:9: note: candidate function not viable: requires 3 arguments, but 1 was provided
int compare(size_type __pos1, size_type __n1, const basic_string& __str) const;
^
/usr/local/miniconda/conda-bld/adios2_1569893413423/_build_env/bin/../include/c++/v1/string:1206:9: note: candidate function not viable: requires 3 arguments, but 1 was provided
int compare(size_type __pos1, size_type __n1, const value_type* __s) const;
^
/usr/local/miniconda/conda-bld/adios2_1569893413423/_build_env/bin/../include/c++/v1/string:1207:9: note: candidate function not viable: requires 4 arguments, but 1 was provided
int compare(size_type __pos1, size_type __n1, const value_type* __s, size_type __n2) const;
^
/usr/local/miniconda/conda-bld/adios2_1569893413423/_build_env/bin/../include/c++/v1/string:1196:9: note: candidate function not viable: requires at least 4 arguments, but 1 was provided
int compare(size_type __pos1, size_type __n1, const basic_string& __str, size_type __pos2, size_type __n2=npos) const;
^
1 error generated.
```https://code.ornl.gov/pnb/ADIOS2/-/issues/1800ZFP not found in 2.5.02019-10-02T06:29:44ZPodhorszki, NorbertZFP not found in 2.5.0*Created by: ax3l*
Hi,
within the release 2.4.0 to 2.5.0, the install of ADIOS2 cannot find zfp anymore.
Related to https://github.com/spack/spack/pull/12987
Probably caused by #1784
With Spack, ZFP 0.5.1-0.5.4 provided and AD...*Created by: ax3l*
Hi,
within the release 2.4.0 to 2.5.0, the install of ADIOS2 cannot find zfp anymore.
Related to https://github.com/spack/spack/pull/12987
Probably caused by #1784
With Spack, ZFP 0.5.1-0.5.4 provided and ADIOS 2.5.0:
```
1 error found in build log:
15 -- Detecting CXX compile features
16 -- Detecting CXX compile features - done
17 -- Found Blosc: /home/axel/src/spack/opt/spack/linux-ubuntu18.04-skylake/gcc-8.3.0/c-blos
c-1.17.0-q5lqzezea6b7b5v4lt2aogurt3k6y3w3/lib/libblosc.so (found suitable version "1.17.0
", minimum required is "1.7")
18 -- Found BZip2: /home/axel/src/spack/opt/spack/linux-ubuntu18.04-skylake/gcc-8.3.0/bzip2-
1.0.8-y3jwkzygasvmix7wsxsp7ughqon54dl5/lib/libbz2.so (found version "1.0.8")
19 -- Looking for BZ2_bzCompressInit
20 -- Looking for BZ2_bzCompressInit - found
>> 21 CMake Error at cmake/DetectOptions.cmake:36 (find_package):
22 Could not find a package configuration file provided by "zfp" (requested
23 version 0.5.1) with any of the following names:
24
25 zfpConfig.cmake
26 zfp-config.cmake
27
```https://code.ornl.gov/pnb/ADIOS2/-/issues/1794cmake not checking for python3-dev dependency2019-09-30T18:09:55ZPodhorszki, Norbertcmake not checking for python3-dev dependency*Created by: williamfgc*
@chuckatkins not sure if you can reproduce, I am not doing anything fancy.
System: Ubuntu 18
CMake version: 3.15.3
```
cmake ../ADIOS2
-- The C compiler identification is GNU 7.4.0
-- The CXX compiler id...*Created by: williamfgc*
@chuckatkins not sure if you can reproduce, I am not doing anything fancy.
System: Ubuntu 18
CMake version: 3.15.3
```
cmake ../ADIOS2
-- The C compiler identification is GNU 7.4.0
-- The CXX compiler identification is GNU 7.4.0
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Could NOT find Blosc (missing: BLOSC_LIBRARY BLOSC_INCLUDE_DIR) (Required is at least version "1.7")
-- Could NOT find BZip2 (missing: BZIP2_LIBRARIES BZIP2_INCLUDE_DIR)
-- Could NOT find zfp (missing: zfp_DIR)
-- Could NOT find SZ (missing: SZ_LIBRARY ZSTD_LIBRARY SZ_INCLUDE_DIR)
-- Could NOT find MGARD (missing: MGARD_LIBRARY BLOSC_LIBRARY MGARD_INCLUDE_DIR)
-- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.11")
-- Could NOT find PNG (missing: PNG_LIBRARY PNG_PNG_INCLUDE_DIR) (Required is at least version "1.6.0")
-- Looking for a Fortran compiler
-- Looking for a Fortran compiler - /usr/bin/f95
-- The Fortran compiler identification is GNU 7.4.0
-- Check for working Fortran compiler: /usr/bin/f95
-- Check for working Fortran compiler: /usr/bin/f95 -- works
-- Detecting Fortran compiler ABI info
-- Detecting Fortran compiler ABI info - done
-- Checking whether /usr/bin/f95 supports Fortran 90
-- Checking whether /usr/bin/f95 supports Fortran 90 -- yes
-- Found MPI_C: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so (found version "3.1")
-- Found MPI_CXX: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so (found version "3.1")
-- Found MPI_Fortran: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_usempif08.so (found version "3.1")
-- Found MPI: TRUE (found version "3.1") found components: C Fortran CXX
-- Found ZeroMQ: /usr/lib/x86_64-linux-gnu/libzmq.so (found suitable version "4.2.5", minimum required is "4.1")
-- Could NOT find DataSpaces (missing: DATASPACES_VERSION DATASPACES_INCLUDE_DIR DATASPACES_LIBRARIES DSPACES_LIBRARY) (Required is at least version "1.8")
-- Could NOT find HDF5 (missing: HDF5_LIBRARIES HDF5_INCLUDE_DIRS C) (found version "")
-- Found PythonInterp: /usr/bin/python3 (found version "3.6.8")
-- Found PythonLibs: /usr/lib/x86_64-linux-gnu/libpython3.6m.so (found version "3.6.8")
-- Found PythonModule_numpy: /usr/lib/python3/dist-packages/numpy
-- Found PythonModule_mpi4py: /usr/lib/python3/dist-packages/mpi4py
-- Found PythonFull: /usr/bin/python3 found components: Interp Libs numpy mpi4py
-- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.1")
-- Checking for module 'libfabric'
-- No package 'libfabric' found
-- Could NOT find LIBFABRIC (missing: LIBFABRIC_LIBRARIES) (Required is at least version "1.6")
-- Could NOT find NVStream (missing: NVSTREAM_LIBRARY NVSTREAM_INCLUDE_DIR)
-- NVSTREAM_FOUND is FALSE, LIB is NVSTREAM_LIBRARY-NOTFOUND
-- Looking for shmget
-- Looking for shmget - found
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- ADIOS2 ThirdParty: Configuring KWSys
-- Checking whether header cstdio is available
-- Checking whether header cstdio is available - yes
-- Checking for Large File Support
-- Checking for Large File Support - yes
-- Checking whether C++ compiler has 'long long'
-- Checking whether C++ compiler has 'long long' - yes
-- Checking whether C++ compiler has '__int64'
-- Checking whether C++ compiler has '__int64' - no
-- Checking whether wstring is available
-- Checking whether wstring is available - yes
-- Checking whether C compiler has ptrdiff_t in stddef.h
-- Checking whether C compiler has ptrdiff_t in stddef.h - yes
-- Checking whether C compiler has ssize_t in unistd.h
-- Checking whether C compiler has ssize_t in unistd.h - yes
-- Checking whether CXX compiler has setenv
-- Checking whether CXX compiler has setenv - yes
-- Checking whether CXX compiler has unsetenv
-- Checking whether CXX compiler has unsetenv - yes
-- Checking whether CXX compiler has environ in stdlib.h
-- Checking whether CXX compiler has environ in stdlib.h - no
-- Checking whether CXX compiler has utimes
-- Checking whether CXX compiler has utimes - yes
-- Checking whether CXX compiler has utimensat
-- Checking whether CXX compiler has utimensat - yes
-- Checking whether CXX compiler struct stat has st_mtim member
-- Checking whether CXX compiler struct stat has st_mtim member - yes
-- Checking whether CXX compiler struct stat has st_mtimespec member
-- Checking whether CXX compiler struct stat has st_mtimespec member - no
-- Checking whether <ext/stdio_filebuf.h> is available
-- Checking whether <ext/stdio_filebuf.h> is available - yes
-- ADIOS2 ThirdParty: Configuring GTest
-- Check if compiler accepts -pthread
-- Check if compiler accepts -pthread - yes
-- ADIOS2 ThirdParty: Configuring pybind11
CMake Error at thirdparty/pybind11/pybind11/tools/FindPythonLibsNew.cmake:95 (message):
Python config failure:
Traceback (most recent call last):
File "<string>", line 1, in <module>
ImportError: cannot import name 'sysconfig'
Call Stack (most recent call first):
thirdparty/pybind11/pybind11/tools/pybind11Tools.cmake:16 (find_package)
thirdparty/pybind11/pybind11/CMakeLists.txt:33 (include)
-- Configuring incomplete, errors occurred!
See also "/home/wgodoy/workspace/ADIOS2-build/CMakeFiles/CMakeOutput.log".
See also "/home/wgodoy/workspace/ADIOS2-build/CMakeFiles/CMakeError.log".
```
https://code.ornl.gov/pnb/ADIOS2/-/issues/1745null pointer in MinMax2019-09-29T02:25:20ZPodhorszki, Norbertnull pointer in MinMax*Created by: philip-davis*
I'm doing a large streaming file run with gray-scott coupled to pdf_calc on Theta, and I am sometimes (not always) seeing pdf_calc crash with many of the following strangely-formatted errors:
```
terminate...*Created by: philip-davis*
I'm doing a large streaming file run with gray-scott coupled to pdf_calc on Theta, and I am sometimes (not always) seeing pdf_calc crash with many of the following strangely-formatted errors:
```
terminate called after throwing an instance of 'terminate called after throwing an instance of 'terminate called after throwing an instance of 'std::invalid_argument'
std::invalid_argument'
std::invalid_argument'
what(): ERROR: found null pointer in call to Variable<T>::MinMax
```
This is using BP4 with the following configuration (I have combined SST and BP4 parameters for reuse:
```
<io name="SimulationOutput">
<engine type="BP4">
<!-- SST engine parameters -->
<parameter key="RendezvousReaderCount" value="1"/>
<parameter key="QueueLimit" value="1"/>
<parameter key="QueueFullPolicy" value="Block"/>
<!-- BP4/SST engine parameters -->
<parameter key="OpenTimeoutSecs" value="900"/>
<parameter key="BeginStepPollingFrequencySecs" value="1" />
<parameter key="SubStreams" value="512"/>
</engine>
</io>
```
This occurs on the first timestep of the reader. The writer runs to completion. For reference, here is some of the pdf_calc code that precedes the MinMax call:
https://github.com/pnorbert/adiosvm/blob/75bf69b13638f7c67981f43d269d2a19e269da20/Tutorial/gray-scott/analysis/pdf_calc.cpp#L182-L216https://code.ornl.gov/pnb/ADIOS2/-/issues/1748bpls is still using MPI?2019-09-27T14:41:33ZPodhorszki, Norbertbpls is still using MPI?*Created by: pnorbert*
As mentioned in #1745, bpls seems to use MPI somewhere in the ADIOS library, even though it is a serial code. How can we debug this and find the place where it happens?
*Created by: pnorbert*
As mentioned in #1745, bpls seems to use MPI somewhere in the ADIOS library, even though it is a serial code. How can we debug this and find the place where it happens?
2.5.0 Production Releasehttps://code.ornl.gov/pnb/ADIOS2/-/issues/1740Make FFS optional at build2019-09-25T17:45:21ZPodhorszki, NorbertMake FFS optional at build*Created by: williamfgc*
Related to #1738 and #1495
@eisenhauer @pnorbert @chuckatkins @JasonRuonanWang since FFS is not officially sanction as pointed out by @eisenhauer. I'd like to propose making it an optional flag `-DADIOS_USE_...*Created by: williamfgc*
Related to #1738 and #1495
@eisenhauer @pnorbert @chuckatkins @JasonRuonanWang since FFS is not officially sanction as pointed out by @eisenhauer. I'd like to propose making it an optional flag `-DADIOS_USE_SST_FFS=OFF`. Thanks.https://code.ornl.gov/pnb/ADIOS2/-/issues/1752Attempting to use an MPI routine after finalizing MPICH2019-09-25T17:42:49ZPodhorszki, NorbertAttempting to use an MPI routine after finalizing MPICH*Created by: philip-davis*
I am seeing this error message on Cori when doing coupled gray-scott runs. I only see this using the BP4 engine, and I only see it on the reader (pdf_calc) side. Here is a tar of my job directory:
[issue2.tar...*Created by: philip-davis*
I am seeing this error message on Cori when doing coupled gray-scott runs. I only see this using the BP4 engine, and I only see it on the reader (pdf_calc) side. Here is a tar of my job directory:
[issue2.tar.gz](https://github.com/ornladios/ADIOS2/files/3622899/issue2.tar.gz)
This is a 256x8 job.https://code.ornl.gov/pnb/ADIOS2/-/issues/778Heat transfer example crashes with SST on Titan2019-09-25T17:24:09ZPodhorszki, NorbertHeat transfer example crashes with SST on Titan*Created by: keichi*
Hi, I'm having trouble running the heat transfer example with SST engine on Titan. The example crashes after a dozens of timesteps. I'm using the current master of ADIOS2 (237f1be25b65035a1f1b5944b276461befd624c9).
...*Created by: keichi*
Hi, I'm having trouble running the heat transfer example with SST engine on Titan. The example crashes after a dozens of timesteps. I'm using the current master of ADIOS2 (237f1be25b65035a1f1b5944b276461befd624c9).
Command
```
aprun -n 64 ./heatTransfer_write_adios2 ./heat_sst.xml foo 8 8 1000 1000 100 100 : -n 16 ./heatTransfer_read ./heat_sst.xml foo.bp bar 4 4
```
Config XML file (same as `examples/heatTransfer/heat_sst_ffs.xml`)
```
<?xml version="1.0"?>
<!-- Config XML file fo the
- heatTransfer_write_adios2
- heatTransfer_read
executables in build/bin -->
<adios-config>
<!--====================================
Configuration for the Writer
====================================-->
<io name="writer">
<engine type="SST">
<parameter key="MarshalMethod" value="FFS"/>
</engine>
</io>
<!--======================================
Configuration for the Reader Input
======================================-->
<io name="readerInput">
<engine type="SST">
<parameter key="MarshalMethod" value="FFS"/>
</engine>
</io>
<!--=======================================
Configuration for the Reader output
=======================================-->
<io name="readerOutput">
<engine type="BPFile">
</engine>
</io>
</adios-config>
```
stdout
https://gist.github.com/keichi/73e4974403cd3f2dc5f4f8f3e0c4e1b9
stderr (SstVerbose=1)
https://gist.github.com/keichi/9e5b9891e5124f9771c063acdb5976b5Eisenhauer, GregEisenhauer, Greghttps://code.ornl.gov/pnb/ADIOS2/-/issues/813heat2d with SST hangs on Titan as it scales2019-09-25T16:42:25ZPodhorszki, Norbertheat2d with SST hangs on Titan as it scales*Created by: jychoi-hpc*
I am trying to run heat2d with SST on Titan. With a small number of processes (say, 4 heat2d processes and 4 analysis processes), it works.
However, with an increased setting (64 head2d and 64 analysis), it ...*Created by: jychoi-hpc*
I am trying to run heat2d with SST on Titan. With a small number of processes (say, 4 heat2d processes and 4 analysis processes), it works.
However, with an increased setting (64 head2d and 64 analysis), it hangs. Here is my aprun command:
```
aprun \
-n 64 simulation/heatSimulation_adios2 heat 8 8 600 300 10 600 :\
-n 64 analysis/heatAnalysis_adios2_stream heat.bp
```
I think this problem is related with my previous problem (a variant of heat2d in which not all processes writes, available on Titan: /lustre/atlas2/csc143/proj-shared/jyc/titan/adios2-heat2d)Eisenhauer, GregEisenhauer, Greghttps://code.ornl.gov/pnb/ADIOS2/-/issues/613Reading more steps than available2019-09-25T16:37:47ZPodhorszki, NorbertReading more steps than available*Created by: pnorbert*
BP file: it returns 0 in the arrays (or does nothing)
HDF5 file: it aborts
ADIOS 1.x gave an error describing what's wrong. With 11 steps in the heat transfer output, the adios 1.x bpls behaves like this when tr...*Created by: pnorbert*
BP file: it returns 0 in the arrays (or does nothing)
HDF5 file: it aborts
ADIOS 1.x gave an error describing what's wrong. With 11 steps in the heat transfer output, the adios 1.x bpls behaves like this when trying to read 2 steps from the last available step:
```
$ bpls -l heat.bp -d -s "10,0,0" -c "2,10,6" --format "%5.2f"
double T 11*{160, 150} = -6.22402 / 7.02874 / null / null
slice (10:11, 0:9, 0:5)
ERROR: Variable T does not have timesteps 10 to 11 (last timestep is 10)
Error when scheduling variable T for reading. errno=-14 : Variable T does not have timesteps 10 to 11 (last timestep is 10)
```
utils/bpls in adios2 behaves like this for a BP file:
```
ADIOS2/build$ ./bin/bpls -l heat.bp -d -s "10,0,0" -c "2,10,6" --format "%5.2f"
double T 11*{160, 150}
slice (10:11, 0:9, 0:5)
(10,0,0) 2.95 2.90 2.85 2.80 2.77 2.73
(10,1,0) 2.90 2.80 2.70 2.62 2.54 2.48
(10,2,0) 2.85 2.70 2.56 2.44 2.32 2.23
(10,3,0) 2.80 2.61 2.43 2.27 2.13 2.01
(10,4,0) 2.76 2.54 2.32 2.13 1.95 1.81
(10,5,0) 2.73 2.47 2.23 2.00 1.81 1.64
(10,6,0) 2.70 2.42 2.15 1.90 1.69 1.50
(10,7,0) 2.68 2.38 2.09 1.83 1.60 1.40
(10,8,0) 2.67 2.35 2.05 1.78 1.54 1.33
(10,9,0) 2.66 2.34 2.03 1.75 1.50 1.30
(11,0,0) 0.00 0.00 0.00 0.00 0.00 0.00
(11,1,0) 0.00 0.00 0.00 0.00 0.00 0.00
(11,2,0) 0.00 0.00 0.00 0.00 0.00 0.00
(11,3,0) 0.00 0.00 0.00 0.00 0.00 0.00
(11,4,0) 0.00 0.00 0.00 0.00 0.00 0.00
(11,5,0) 0.00 0.00 0.00 0.00 0.00 0.00
(11,6,0) 0.00 0.00 0.00 0.00 0.00 0.00
(11,7,0) 0.00 0.00 0.00 0.00 0.00 0.00
(11,8,0) 0.00 0.00 0.00 0.00 0.00 0.00
(11,9,0) 0.00 0.00 0.00 0.00 0.00 0.00
```
and on a HDF5 file, it aborts:
```
ADIOS2/build$ ./bin/bpls -l heat.h5 -d -s "10,0,0" -c "2,10,6" --format "%5.2f"
double T 11*{160, 150}
slice (10:11, 0:9, 0:5)
terminate called after throwing an instance of 'std::ios_base::failure[abi:cxx11]'
what(): ERROR: given time step is more than actual known steps.: iostream error
[adiosVM:32695] *** Process received signal ***
[adiosVM:32695] Signal: Aborted (6)
[adiosVM:32695] Signal code: (-6)
[adiosVM:32695] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x11390)[0x7f2d74db3390]
[adiosVM:32695] [ 1] /lib/x86_64-linux-gnu/libc.so.6(gsignal+0x38)[0x7f2d74a0d428]
[adiosVM:32695] [ 2] /lib/x86_64-linux-gnu/libc.so.6(abort+0x16a)[0x7f2d74a0f02a]
[adiosVM:32695] [ 3] /usr/lib/x86_64-linux-gnu/libstdc++.so.6(_ZN9__gnu_cxx27__verbose_terminate_handlerEv+0x16d)[0x7f2d7526484d]
[adiosVM:32695] [ 4] /usr/lib/x86_64-linux-gnu/libstdc++.so.6(+0x8d6b6)[0x7f2d752626b6]
[adiosVM:32695] [ 5] /usr/lib/x86_64-linux-gnu/libstdc++.so.6(+0x8d701)[0x7f2d75262701]
[adiosVM:32695] [ 6] /usr/lib/x86_64-linux-gnu/libstdc++.so.6(+0x8d919)[0x7f2d75262919]
[adiosVM:32695] [ 7] /home/adios/work/ADIOS2/build/lib/libadios2.so.2(_ZN6adios27interop10HDF5Common12SetAdiosStepEi+0x167)[0x7f2d761e0a9b]
[adiosVM:32695] [ 8] /home/adios/work/ADIOS2/build/lib/libadios2.so.2(_ZN6adios211HDF5ReaderP10UseHDFReadIdEEvRNS_8VariableIT_EEPS3_i+0x580)[0x7f2d761da92a]
[adiosVM:32695] [ 9] /home/adios/work/ADIOS2/build/lib/libadios2.so.2(_ZN6adios211HDF5ReaderP13GetSyncCommonIdEEvRNS_8VariableIT_EEPS3_+0x40)[0x7f2d761dde00]
[adiosVM:32695] [10] /home/adios/work/ADIOS2/build/lib/libadios2.so.2(_ZN6adios211HDF5ReaderP9DoGetSyncERNS_8VariableIdEEPd+0x2b)[0x7f2d761d1b4b]
[adiosVM:32695] [11] /home/adios/work/ADIOS2/build/lib/libadios2.so.2(_ZN6adios26Engine7GetSyncIdEEvRNS_8VariableIT_EEPS3_+0x3fc)[0x7f2d75fc149c]
[adiosVM:32695] [12] ./bin/bpls[0x4810c2]
[adiosVM:32695] [13] ./bin/bpls[0x471eb2]
[adiosVM:32695] [14] ./bin/bpls[0x4698ac]
[adiosVM:32695] [15] ./bin/bpls[0x46a39e]
[adiosVM:32695] [16] ./bin/bpls[0x468627]
[adiosVM:32695] [17] ./bin/bpls[0x46cbdc]
[adiosVM:32695] [18] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0)[0x7f2d749f8830]
[adiosVM:32695] [19] ./bin/bpls[0x467a09]
[adiosVM:32695] *** End of error message ***
```
For the latter one, the bug is probably in HDF5Common::SetAdiosStep(int step), the condition
```if (step >= m_NumAdiosSteps)```
passing for step one bigger than the last valid step index (NumAdiosSteps-1)
https://code.ornl.gov/pnb/ADIOS2/-/issues/568Cannot read data from ADIOS1 BP file which has no subfiles2019-09-25T16:34:31ZPodhorszki, NorbertCannot read data from ADIOS1 BP file which has no subfiles*Created by: pnorbert*
ADIOS 1.x MPI transport produces a BP file with data in it. No subfiles. The subfile index for variables is -1.
ADIOS 2 misinterprets that -1 and still tries to read from a subfile:
ERROR: couldn't open fil...*Created by: pnorbert*
ADIOS 1.x MPI transport produces a BP file with data in it. No subfiles. The subfile index for variables is -1.
ADIOS 2 misinterprets that -1 and still tries to read from a subfile:
ERROR: couldn't open file heat.bp.dir/heat.bp.4294967295, check permissions or path existence, in call to POSIX open
: iostream error
adios@adiosVM:~/work/adiosvm/Tutorial/heat_transfer$ ls -l heat.bp
-rw-rw-r-- 1 adios adios 2409312 Apr 23 09:43 heat.bp
https://code.ornl.gov/pnb/ADIOS2/-/issues/220Add support for version checking in FindZFP2019-09-25T16:32:51ZPodhorszki, NorbertAdd support for version checking in FindZFP*Created by: chuckatkins*
Minimum version required is 0.5.1, but FindZFP doesn't currently handle version checking*Created by: chuckatkins*
Minimum version required is 0.5.1, but FindZFP doesn't currently handle version checking2.5.0 Production Releasehttps://code.ornl.gov/pnb/ADIOS2/-/issues/1765POSIX Transport creates file on Open() without Flush() 2019-09-19T20:20:49ZPodhorszki, NorbertPOSIX Transport creates file on Open() without Flush() *Created by: philip-davis*
The open() system call can create the file on disk immediately. To demonstrate this, log into two different login nodes on, for example, Cori and run this code on one of them:
```
#include <sys/types.h>
#...*Created by: philip-davis*
The open() system call can create the file on disk immediately. To demonstrate this, log into two different login nodes on, for example, Cori and run this code on one of them:
```
#include <sys/types.h>
#include <sys/stat.h>
#include <fcntl.h>
#include <stdlib.h>
#include <unistd.h>
int main()
{
int fd;
struct stat st;
open("abc.txt", O_WRONLY | O_CREAT | O_TRUNC, 0666);
sleep(100);
return(0);
}
```
abc.txt will be visible on the other login node immediately, both for NFS and Lustre file systems.
The reason I bring this up is that this open() call[ is the same as the one used by FilePOSIX::Open() when openMode is Mode::Write.](https://github.com/ornladios/ADIOS2/blob/7da36fbec480d531119fadd7e655eb730e913878/source/adios2/toolkit/transport/file/FilePOSIX.cpp#L51) If I'm reading the code correctly, FilePOSIX is the default Transport library, including for BP4. This matters for the File Metadata Index. Even though [we wait until after writing the header to do a flush](https://github.com/ornladios/ADIOS2/blob/7da36fbec480d531119fadd7e655eb730e913878/source/adios2/engine/bp4/BP4Writer.cpp#L215-L230), that flush is a no-op for POSIX, and the zero-length file has already been created.
This is, in turn, a problem because the reader could see the zero-length metadata index file, and then interpreting the header as a new timestep. I expect ParseMetadata would fail noisily in this case, but I haven't looked closely enough at the code to know that for sure.https://code.ornl.gov/pnb/ADIOS2/-/issues/1760Current master is broken when configuring with SZ2019-09-19T02:30:50ZPodhorszki, NorbertCurrent master is broken when configuring with SZ*Created by: williamfgc*
the `fortran_add_test_helper` function doesn't handle the BPWriteReadSZ* tests in the operation subdirectory. The following message appears:
```
Features:
Library Type: shared
Build Type: Debug
...*Created by: williamfgc*
the `fortran_add_test_helper` function doesn't handle the BPWriteReadSZ* tests in the operation subdirectory. The following message appears:
```
Features:
Library Type: shared
Build Type: Debug
Testing: ON
Build Options:
Blosc : ON
BZip2 : ON
ZFP : OFF
SZ : ON
MGARD : ON
PNG : ON
MPI : ON
DataMan : OFF
Table : OFF
SSC : OFF
SST : ON
DataSpaces: OFF
ZeroMQ : ON
HDF5 : ON
Python : ON
Fortran : ON
SysVShMem: ON
Profiling: ON
Endian_Reverse: OFF
RDMA Transport for Staging: Unconfigured
-- Configuring done
CMake Error at testing/adios2/bindings/fortran/CMakeLists.txt:9 (add_executable):
Cannot find source file:
TestBPWriteReadSZ3D.F90
Tried extensions .c .C .c++ .cc .cpp .cxx .cu .m .M .mm .h .hh .h++ .hm
.hpp .hxx .in .txx
Call Stack (most recent call first):
testing/adios2/bindings/fortran/CMakeLists.txt:76 (fortran_add_test_helper)
CMake Error at testing/adios2/bindings/fortran/CMakeLists.txt:9 (add_executable):
Cannot find source file:
TestBPWriteReadSZ2D.F90
Tried extensions .c .C .c++ .cc .cpp .cxx .cu .m .M .mm .h .hh .h++ .hm
.hpp .hxx .in .txx
Call Stack (most recent call first):
testing/adios2/bindings/fortran/CMakeLists.txt:75 (fortran_add_test_helper)
CMake Error at testing/adios2/bindings/fortran/CMakeLists.txt:9 (add_executable):
No SOURCES given to target: Test.Bindings.Fortran.BPWriteReadSZ3D
Call Stack (most recent call first):
testing/adios2/bindings/fortran/CMakeLists.txt:76 (fortran_add_test_helper)
CMake Error at testing/adios2/bindings/fortran/CMakeLists.txt:9 (add_executable):
No SOURCES given to target: Test.Bindings.Fortran.BPWriteReadSZ2D
Call Stack (most recent call first):
testing/adios2/bindings/fortran/CMakeLists.txt:75 (fortran_add_test_helper)
CMake Generate step failed. Build files cannot be regenerated correctly.
```
2.5.0 Production Releasehttps://code.ornl.gov/pnb/ADIOS2/-/issues/1742Current master is broken when configuring with zfp2019-09-19T02:30:34ZPodhorszki, NorbertCurrent master is broken when configuring with zfp*Created by: williamfgc*
when using `-DADIOS2_USE_ZFP=ON` the following error shows up:
```
-- Verifying Fortran/CXX Compiler Compatibility - Success
CMake Error at testing/examples/heatTransfer/TestBPFileMx1_zfp.cmake:6 (include):...*Created by: williamfgc*
when using `-DADIOS2_USE_ZFP=ON` the following error shows up:
```
-- Verifying Fortran/CXX Compiler Compatibility - Success
CMake Error at testing/examples/heatTransfer/TestBPFileMx1_zfp.cmake:6 (include):
include could not find load file:
ADIOS2Functions
Call Stack (most recent call first):
testing/examples/heatTransfer/CMakeLists.txt:13 (include)
CMake Error at cmake/ADIOSFunctions.cmake:165 (set_property):
set_property given TEST names that do not exist:
HeatTransfer.BP3.zfp.Mx1.Validate
Call Stack (most recent call first):
testing/examples/heatTransfer/TestBPFileMx1_zfp.cmake:33 (SetupTestPipeline)
testing/examples/heatTransfer/CMakeLists.txt:13 (include)
CMake Error at cmake/ADIOSFunctions.cmake:168 (set_property):
set_property given TEST names that do not exist:
HeatTransfer.BP3.zfp.Mx1.Validate
Call Stack (most recent call first):
testing/examples/heatTransfer/TestBPFileMx1_zfp.cmake:33 (SetupTestPipeline)
testing/examples/heatTransfer/CMakeLists.txt:13 (include)
CMake Error at cmake/ADIOSFunctions.cmake:171 (set_property):
set_property given TEST names that do not exist:
HeatTransfer.BP3.zfp.Mx1.Validate
Call Stack (most recent call first):
testing/examples/heatTransfer/TestBPFileMx1_zfp.cmake:33 (SetupTestPipeline)
testing/examples/heatTransfer/CMakeLists.txt:13 (include)
CMake Error at cmake/ADIOSFunctions.cmake:165 (set_property):
set_property given TEST names that do not exist:
HeatTransfer.BP4.zfp.Mx1.Validate
Call Stack (most recent call first):
testing/examples/heatTransfer/TestBPFileMx1_zfp.cmake:61 (SetupTestPipeline)
testing/examples/heatTransfer/CMakeLists.txt:13 (include)
CMake Error at cmake/ADIOSFunctions.cmake:168 (set_property):
set_property given TEST names that do not exist:
HeatTransfer.BP4.zfp.Mx1.Validate
Call Stack (most recent call first):
testing/examples/heatTransfer/TestBPFileMx1_zfp.cmake:61 (SetupTestPipeline)
testing/examples/heatTransfer/CMakeLists.txt:13 (include)
CMake Error at cmake/ADIOSFunctions.cmake:171 (set_property):
set_property given TEST names that do not exist:
HeatTransfer.BP4.zfp.Mx1.Validate
Call Stack (most recent call first):
testing/examples/heatTransfer/TestBPFileMx1_zfp.cmake:61 (SetupTestPipeline)
testing/examples/heatTransfer/CMakeLists.txt:13 (include)
-- Found MPI: TRUE (found version "3.1") found components: C
ADIOS2 build configuration:
ADIOS Version: 2.4.0.442
C++ Compiler : GNU 7.4.0
/usr/bin/c++
Fortran Compiler : GNU 7.4.0
/usr/bin/f95
Installation prefix: /home/wgodoy/tmp/adios2
bin: bin
lib: lib
include: include
cmake: lib/cmake/adios2
python: lib/python3.6/site-packages
Features:
Library Type: shared
Build Type: Debug
Testing: ON
Build Options:
Blosc : ON
BZip2 : ON
ZFP : ON
SZ : ON
MGARD : ON
PNG : ON
MPI : ON
DataMan : OFF
Table : OFF
SSC : OFF
SST : ON
DataSpaces: OFF
ZeroMQ : ON
HDF5 : ON
Python : ON
Fortran : ON
SysVShMem: ON
Profiling: ON
Endian_Reverse: OFF
RDMA Transport for Staging: Unconfigured
-- Configuring incomplete, errors occurred!
See also "/home/wgodoy/tmp/ADIOS2-build/CMakeFiles/CMakeOutput.log".
See also "/home/wgodoy/tmp/ADIOS2-build/CMakeFiles/CMakeError.log".
```https://code.ornl.gov/pnb/ADIOS2/-/issues/1723Segmentation fault with helloBPWriter.py on cori2019-09-18T15:14:34ZPodhorszki, NorbertSegmentation fault with helloBPWriter.py on cori*Created by: rkube*
I'm trying to run the helloBPWriter.py on cori and get a segmentation fault.
This is a self-compiled version of adios2 using icc.
Command used:
$ mpirun -n 1 python -m mpi4py helloBPWriter.py
libhugetlbfs [co...*Created by: rkube*
I'm trying to run the helloBPWriter.py on cori and get a segmentation fault.
This is a self-compiled version of adios2 using icc.
Command used:
$ mpirun -n 1 python -m mpi4py helloBPWriter.py
libhugetlbfs [cori10:3626]: WARNING: Hugepage size 2097152 unavailablelibhugetlbfs [cori10:3626]: WARNING: New heap segment map at 0x10000000000 failed: Cannot allocate memory
[cori10:03626] *** Process received signal ***
[cori10:03626] Signal: Segmentation fault (11)
[cori10:03626] Signal code: Address not mapped (1)
[cori10:03626] Failing at address: 0xac2473a8
[cori10:03626] [ 0] /lib64/libpthread.so.0(+0x12360)[0x2aaaaace5360]
[cori10:03626] [ 1] /global/common/software/m3169/openmpi/3.1.4/intel/lib/libmpi.so.40(MPI_Comm_dup+0x19e)[0x2aaaabfa528e]
[cori10:03626] [ 2] /global/homes/r/rkube/local/lib64/libadios2.so.2(_ZN6adios26helper4Comm9DuplicateEi+0x13)[0x2aaaee350d23]
[cori10:03626] [ 3] /global/homes/r/rkube/local/lib64/libadios2.so.2(_ZN6adios24core5ADIOSC1ENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEibS7_+0xbe)[0x2aaaee18ea1e]
[cori10:03626] [ 4] /global/homes/r/rkube/local/lib64/python3.7/site-packages/adios2.cpython-37m-x86_64-linux-gnu.so(+0x20065f0d)[0x2aaacdf0ff0d]
[cori10:03626] [ 5] /global/homes/r/rkube/local/lib64/python3.7/site-packages/adios2.cpython-37m-x86_64-linux-gnu.so(+0x20059fad)[0x2aaacdf03fad]
[cori10:03626] [ 6] /global/homes/r/rkube/local/lib64/python3.7/site-packages/adios2.cpython-37m-x86_64-linux-gnu.so(+0x20066c7d)[0x2aaacdf10c7d]
[cori10:03626] [ 7] python(_PyMethodDef_RawFastCallDict+0x24d)[0x55555568963d]
[cori10:03626] [ 8] python(_PyCFunction_FastCallDict+0x21)[0x5555556897c1]
[cori10:03626] [ 9] python(_PyObject_Call_Prepend+0x63)[0x555555687e53]
[cori10:03626] [10] python(PyObject_Call+0x6e)[0x55555567adbe]
[cori10:03626] [11] python(+0x9e214)[0x5555555f2214]
[cori10:03626] [12] python(_PyObject_FastCallKeywords+0x128)[0x5555556c0588]
[cori10:03626] [13] python(_PyEval_EvalFrameDefault+0x52f8)[0x5555557246e8]
[cori10:03626] [14] python(_PyEval_EvalCodeWithName+0x2f9)[0x555555668539]
[cori10:03626] [15] python(PyEval_EvalCodeEx+0x44)[0x555555669424]
[cori10:03626] [16] python(PyEval_EvalCode+0x1c)[0x55555566944c]
[cori10:03626] [17] python(+0x1dae81)[0x55555572ee81]
[cori10:03626] [18] python(_PyMethodDef_RawFastCallKeywords+0xe9)[0x5555556b85d9]
[cori10:03626] [19] python(_PyCFunction_FastCallKeywords+0x21)[0x5555556b8861]
[cori10:03626] [20] python(_PyEval_EvalFrameDefault+0x47a4)[0x555555723b94]
[cori10:03626] [21] python(_PyEval_EvalCodeWithName+0x2f9)[0x555555668539]
[cori10:03626] [22] python(_PyFunction_FastCallKeywords+0x325)[0x5555556b7ef5]
[cori10:03626] [23] python(_PyEval_EvalFrameDefault+0x416)[0x55555571f806]
[cori10:03626] [24] python(_PyEval_EvalCodeWithName+0x2f9)[0x555555668539]
[cori10:03626] [25] python(_PyFunction_FastCallKeywords+0x387)[0x5555556b7f57]
[cori10:03626] [26] python(_PyEval_EvalFrameDefault+0x14dc)[0x5555557208cc]
[cori10:03626] [27] python(_PyEval_EvalCodeWithName+0x2f9)[0x555555668539]
[cori10:03626] [28] python(_PyFunction_FastCallKeywords+0x387)[0x5555556b7f57]
[cori10:03626] [29] python(_PyEval_EvalFrameDefault+0x14dc)[0x5555557208cc]
[cori10:03626] *** End of error message ***
(delta) rkube@cori10:~/repos/ADIOS2/examples/hello/bpWriter> python --version
Python 3.7.4
(delta) rkube@cori10:~/repos/ADIOS2/examples/hello/bpWriter> module list
Currently Loaded Modulefiles:
1) modules/3.2.11.1 13) job/2.2.4-7.0.0.1_3.30__g36b56f4.ari
2) nsg/1.2.0 14) dvs/2.11_2.2.137-7.0.0.1_10.1__g04d35b33
3) intel/19.0.3.199 15) alps/6.6.50-7.0.0.1_3.35__g962f7108.ari
4) craype-network-aries 16) rca/2.2.20-7.0.0.1_4.34__g8e3fb5b.ari
5) craype/2.5.18 17) atp/2.1.3
6) cray-libsci/19.02.1 18) PrgEnv-intel/6.0.5
7) udreg/2.3.2-7.0.0.1_4.27__g8175d3d.ari 19) craype-haswell
8) ugni/6.0.14.0-7.0.0.1_7.30__ge78e5b0.ari 20) cray-mpich/7.7.6
9) pmi/5.0.14 21) craype-hugepages2M
10) dmapp/7.1.1-7.0.0.1_5.20__g25e5077.ari 22) cmake/3.14.4
11) gni-headers/5.0.12.0-7.0.0.1_7.39__g3b1768f.ari 23) python/3.7-anaconda-2019.07
12) xpmem/2.2.17-7.0.0.1_3.24__g7acee3a.ari 24) openmpi/3.1.4
https://code.ornl.gov/pnb/ADIOS2/-/issues/1727Compression examples and shared-memory2019-09-10T09:30:10ZPodhorszki, NorbertCompression examples and shared-memory*Created by: tobiasrau*
Unfortunately, I couldn't find any examples on how to use the encoding or the shared memory implementation offered by ADIOS2.
Maybe I've just not found the right page in the documentation or in the examples of t...*Created by: tobiasrau*
Unfortunately, I couldn't find any examples on how to use the encoding or the shared memory implementation offered by ADIOS2.
Maybe I've just not found the right page in the documentation or in the examples of the repository.
However, it would be nice to get some more information about this topic.https://code.ornl.gov/pnb/ADIOS2/-/issues/1716SST parameter value uppercase/lowercase problem2019-09-05T19:36:43ZPodhorszki, NorbertSST parameter value uppercase/lowercase problem*Created by: pnorbert*
I observed that FirstTimestepPrecious, "TRUE" is not working, while "true" does. The documentation btw shows "TRUE" and "yes" as examples. Values should be converted to lowercase before comparing them so that all ...*Created by: pnorbert*
I observed that FirstTimestepPrecious, "TRUE" is not working, while "true" does. The documentation btw shows "TRUE" and "yes" as examples. Values should be converted to lowercase before comparing them so that all bool flags work the same.
Another discrepancy is that some flags are On/Off (BP), others are yes/no or true/false. But this ticket is just pointing out the problem in SST.
2.5.0 Production ReleaseEisenhauer, GregEisenhauer, Greghttps://code.ornl.gov/pnb/ADIOS2/-/issues/1699Libfabric Dependency Detection2019-09-04T16:40:46ZPodhorszki, NorbertLibfabric Dependency Detection*Created by: philip-davis*
I am having an issue building on Cori with libfabric support. I believe this comes down to something I am doing wrong in FindLIBFABRIC.cmake, but I can't figure out what. I am seeing this:
```
[ 40%] Linki...*Created by: philip-davis*
I am having an issue building on Cori with libfabric support. I believe this comes down to something I am doing wrong in FindLIBFABRIC.cmake, but I can't figure out what. I am seeing this:
```
[ 40%] Linking CXX executable ../../../../../bin/sst_conn_tool
/usr/bin/ld: cannot find -lpkgcfg_lib_PC_LIBFABRIC_atomic-NOTFOUND
/usr/bin/ld: /global/homes/p/pdavis/cori/sw/libfabric/gnu/lib/libfabric.a(src_libfabric_la-fabric.o): in function `fi_ini':
fabric.c:(.text+0xaa2): warning: Using 'dlopen' in statically linked applications requires at runtime the shared libraries from the glibc version used for linking
collect2: error: ld returned 1 exit status
make[2]: *** [source/adios2/toolkit/sst/util/CMakeFiles/sst_conn_tool.dir/build.make:100: bin/sst_conn_tool] Error 1
make[1]: *** [CMakeFiles/Makefile2:2007: source/adios2/toolkit/sst/util/CMakeFiles/sst_conn_tool.dir/all] Error 2
make: *** [Makefile:141: all] Error 2
```
Which looks to me like cmake is inducing a failure because it thought it needed to find the absolute path libatomic using pkg-config, but couldn't. I see this in `CMakeCache.txt`:
```
//Path to a library.
pkgcfg_lib_PC_LIBFABRIC_alpslli:FILEPATH=/opt/cray/alps/6.6.50-7.0.0.1_3.35__g962f7108.ari/lib64/libalpslli.a
//Path to a library.
pkgcfg_lib_PC_LIBFABRIC_alpsutil:FILEPATH=/opt/cray/alps/6.6.50-7.0.0.1_3.35__g962f7108.ari/lib64/libalpsutil.a
//Path to a library.
pkgcfg_lib_PC_LIBFABRIC_atomic:FILEPATH=pkgcfg_lib_PC_LIBFABRIC_atomic-NOTFOUND
//Path to a library.
pkgcfg_lib_PC_LIBFABRIC_dl:FILEPATH=/usr/lib64/libdl.a
//Path to a library.
pkgcfg_lib_PC_LIBFABRIC_fabric:FILEPATH=/global/homes/p/pdavis/cori/sw/libfabric/gnu/lib/libfabric.a
//Path to a library.
pkgcfg_lib_PC_LIBFABRIC_pthread:FILEPATH=/usr/lib64/libpthread.a
//Path to a library.
pkgcfg_lib_PC_LIBFABRIC_udreg:FILEPATH=/opt/cray/udreg/2.3.2-7.0.0.1_4.27__g8175d3d.ari/lib64/libudreg.a
//Path to a library.
pkgcfg_lib_PC_LIBFABRIC_ugni:FILEPATH=/opt/cray/ugni/6.0.14.0-7.0.0.1_7.30__ge78e5b0.ari/lib64/libugni.a
```
libfabric.pc looks like:
```
prefix=/global/homes/p/pdavis/cori/sw/libfabric/gnu
exec_prefix=${prefix}
libdir=${exec_prefix}/lib
includedir=${prefix}/include
Name: libfabric
Description: OFI-WG libfabric
URL: https://github.com/ofiwg/libfabric.git
Version: 1.7.2
Requires:
Cflags: -I${includedir}
Libs: -L${libdir} -lfabric -L/opt/cray/xpmem/2.2.17-7.0.0.1_3.24__g7acee3a.ari/lib64 -lxpmem -L/opt/cray/udreg/2.3.2-7.0.0.1_4.27__g8175d3d.ari/lib64 -ludreg -L/opt/cray/alps/6.6.50-7.0.0.1_3.35__g962f7108.ari/lib64 -lalpsutil -lalpslli -L/opt/cray/ugni/6.0.14.0-7.0.0.1_7.30__ge78e5b0.ari/lib64 -lugni -latomic -lpthread -ldl
Libs.private: -L/opt/cray/xpmem/2.2.17-7.0.0.1_3.24__g7acee3a.ari/lib64 -lxpmem -L/opt/cray/udreg/2.3.2-7.0.0.1_4.27__g8175d3d.ari/lib64 -ludreg -L/opt/cray/alps/6.6.50-7.0.0.1_3.35__g962f7108.ari/lib64 -lalpsutil -lalpslli -L/opt/cray/ugni/6.0.14.0-7.0.0.1_7.30__ge78e5b0.ari/lib64 -lugni -latomic -lpthread -ldl
Requires.private:
```
The absolute path of libatomic is `/opt/gcc/8.2.0/snos/lib64/libatomic.a`, so there's not enough information in libfabric.pc to find it, however, `/opt/gcc/8.2.0/snos/lib64` is in the LIBRARY_PATH of the cc wrapper, and I can link against libatomic:
```
pdavis@cori02:~/tests> cc -v atomic.c -latomic
Using built-in specs.
COLLECT_GCC=/opt/gcc/8.2.0/bin/../snos/bin/gcc
COLLECT_LTO_WRAPPER=/opt/gcc/8.2.0/snos/libexec/gcc/x86_64-suse-linux/8.2.0/lto-wrapper
Target: x86_64-suse-linux
Configured with: ../cray-gcc-8.2.0-201811010913.df0113f60eb17/configure --prefix=/opt/gcc/8.2.0/snos --disable-nls --libdir=/opt/gcc/8.2.0/snos/lib --enable-languages=c,c++,fortran --with-gxx-include-dir=/opt/gcc/8.2.0/snos/include/g++ --with-slibdir=/opt/gcc/8.2.0/snos/lib --with-system-zlib --enable-shared --enable-__cxa_atexit --build=x86_64-suse-linux --with-ppl --with-cloog --disable-multilib
Thread model: posix
gcc version 8.2.0 20180726 (Cray Inc.) (GCC)
COLLECT_GCC_OPTIONS='-march=core-avx2' '-static' '-D' '__CRAYXC' '-D' '__CRAY_HASWELL' '-D' '__CRAYXT_COMPUTE_LINUX_TARGET' '-u' 'pthread_mutex_destroy' '-D' '__TARGET_LINUX__' '-v' '-I' '/opt/cray/pe/libsci/19.02.1/GNU/8.1/x86_64/include' '-I' '/opt/cray/pe/mpt/7.7.6/gni/mpich-gnu/8.2/include' '-I' '/opt/cray/rca/2.2.20-7.0.0.1_4.34__g8e3fb5b.ari/include' '-I' '/opt/cray/alps/6.6.50-7.0.0.1_3.35__g962f7108.ari/include' '-I' '/opt/cray/xpmem/2.2.17-7.0.0.1_3.24__g7acee3a.ari/include' '-I' '/opt/cray/gni-headers/5.0.12.0-7.0.0.1_7.39__g3b1768f.ari/include' '-I' '/opt/cray/pe/pmi/5.0.14/include' '-I' '/opt/cray/ugni/6.0.14.0-7.0.0.1_7.30__ge78e5b0.ari/include' '-I' '/opt/cray/udreg/2.3.2-7.0.0.1_4.27__g8175d3d.ari/include' '-I' '/opt/cray/wlm_detect/1.3.3-7.0.0.1_3.20__g7109084.ari/include' '-I' '/opt/cray/krca/2.2.5-7.0.0.1_4.34__g92086a7.ari/include' '-I' '/opt/cray-hss-devel/9.0.0/include' '-L/opt/cray/pe/libsci/19.02.1/GNU/8.1/x86_64/lib' '-L/opt/cray/dmapp/default/lib64' '-L/opt/cray/pe/mpt/7.7.6/gni/mpich-gnu/8.2/lib' '-L/opt/cray/rca/2.2.20-7.0.0.1_4.34__g8e3fb5b.ari/lib64' '-L/opt/cray/alps/6.6.50-7.0.0.1_3.35__g962f7108.ari/lib64' '-L/opt/cray/xpmem/2.2.17-7.0.0.1_3.24__g7acee3a.ari/lib64' '-L/opt/cray/pe/pmi/5.0.14/lib64' '-L/opt/cray/ugni/6.0.14.0-7.0.0.1_7.30__ge78e5b0.ari/lib64' '-L/opt/cray/udreg/2.3.2-7.0.0.1_4.27__g8175d3d.ari/lib64' '-L/opt/cray/pe/atp/2.1.3/libApp' '-L/opt/cray/wlm_detect/1.3.3-7.0.0.1_3.20__g7109084.ari/lib64'
/opt/gcc/8.2.0/snos/libexec/gcc/x86_64-suse-linux/8.2.0/cc1 -quiet -v -I /opt/cray/pe/libsci/19.02.1/GNU/8.1/x86_64/include -I /opt/cray/pe/mpt/7.7.6/gni/mpich-gnu/8.2/include -I /opt/cray/rca/2.2.20-7.0.0.1_4.34__g8e3fb5b.ari/include -I /opt/cray/alps/6.6.50-7.0.0.1_3.35__g962f7108.ari/include -I /opt/cray/xpmem/2.2.17-7.0.0.1_3.24__g7acee3a.ari/include -I /opt/cray/gni-headers/5.0.12.0-7.0.0.1_7.39__g3b1768f.ari/include -I /opt/cray/pe/pmi/5.0.14/include -I /opt/cray/ugni/6.0.14.0-7.0.0.1_7.30__ge78e5b0.ari/include -I /opt/cray/udreg/2.3.2-7.0.0.1_4.27__g8175d3d.ari/include -I /opt/cray/wlm_detect/1.3.3-7.0.0.1_3.20__g7109084.ari/include -I /opt/cray/krca/2.2.5-7.0.0.1_4.34__g92086a7.ari/include -I /opt/cray-hss-devel/9.0.0/include -D __CRAYXC -D __CRAY_HASWELL -D __CRAYXT_COMPUTE_LINUX_TARGET -D __TARGET_LINUX__ atomic.c -quiet -dumpbase atomic.c -march=core-avx2 -auxbase atomic -version -o /tmp/ccwl9GA7.s
GNU C17 (GCC) version 8.2.0 20180726 (Cray Inc.) (x86_64-suse-linux)
compiled by GNU C version 8.2.0 20180726 (Cray Inc.), GMP version 6.0.0, MPFR version 3.1.3, MPC version 1.0.3, isl version isl-0.15-GMP
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
ignoring nonexistent directory "/opt/gcc/8.2.0/snos/lib/gcc/x86_64-suse-linux/8.2.0/../../../../x86_64-suse-linux/include"
#include "..." search starts here:
#include <...> search starts here:
/opt/cray/pe/libsci/19.02.1/GNU/8.1/x86_64/include
/opt/cray/pe/mpt/7.7.6/gni/mpich-gnu/8.2/include
/opt/cray/rca/2.2.20-7.0.0.1_4.34__g8e3fb5b.ari/include
/opt/cray/alps/6.6.50-7.0.0.1_3.35__g962f7108.ari/include
/opt/cray/xpmem/2.2.17-7.0.0.1_3.24__g7acee3a.ari/include
/opt/cray/gni-headers/5.0.12.0-7.0.0.1_7.39__g3b1768f.ari/include
/opt/cray/pe/pmi/5.0.14/include
/opt/cray/ugni/6.0.14.0-7.0.0.1_7.30__ge78e5b0.ari/include
/opt/cray/udreg/2.3.2-7.0.0.1_4.27__g8175d3d.ari/include
/opt/cray/wlm_detect/1.3.3-7.0.0.1_3.20__g7109084.ari/include
/opt/cray/krca/2.2.5-7.0.0.1_4.34__g92086a7.ari/include
/opt/cray-hss-devel/9.0.0/include
/opt/gcc/8.2.0/snos/lib/gcc/x86_64-suse-linux/8.2.0/include
/usr/local/include
/opt/gcc/8.2.0/snos/include
/opt/gcc/8.2.0/snos/lib/gcc/x86_64-suse-linux/8.2.0/include-fixed
/usr/include
End of search list.
GNU C17 (GCC) version 8.2.0 20180726 (Cray Inc.) (x86_64-suse-linux)
compiled by GNU C version 8.2.0 20180726 (Cray Inc.), GMP version 6.0.0, MPFR version 3.1.3, MPC version 1.0.3, isl version isl-0.15-GMP
GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072
Compiler executable checksum: af69ce7fa3d5dbba875fe0994824dbac
COLLECT_GCC_OPTIONS='-march=core-avx2' '-static' '-D' '__CRAYXC' '-D' '__CRAY_HASWELL' '-D' '__CRAYXT_COMPUTE_LINUX_TARGET' '-u' 'pthread_mutex_destroy' '-D' '__TARGET_LINUX__' '-v' '-I' '/opt/cray/pe/libsci/19.02.1/GNU/8.1/x86_64/include' '-I' '/opt/cray/pe/mpt/7.7.6/gni/mpich-gnu/8.2/include' '-I' '/opt/cray/rca/2.2.20-7.0.0.1_4.34__g8e3fb5b.ari/include' '-I' '/opt/cray/alps/6.6.50-7.0.0.1_3.35__g962f7108.ari/include' '-I' '/opt/cray/xpmem/2.2.17-7.0.0.1_3.24__g7acee3a.ari/include' '-I' '/opt/cray/gni-headers/5.0.12.0-7.0.0.1_7.39__g3b1768f.ari/include' '-I' '/opt/cray/pe/pmi/5.0.14/include' '-I' '/opt/cray/ugni/6.0.14.0-7.0.0.1_7.30__ge78e5b0.ari/include' '-I' '/opt/cray/udreg/2.3.2-7.0.0.1_4.27__g8175d3d.ari/include' '-I' '/opt/cray/wlm_detect/1.3.3-7.0.0.1_3.20__g7109084.ari/include' '-I' '/opt/cray/krca/2.2.5-7.0.0.1_4.34__g92086a7.ari/include' '-I' '/opt/cray-hss-devel/9.0.0/include' '-L/opt/cray/pe/libsci/19.02.1/GNU/8.1/x86_64/lib' '-L/opt/cray/dmapp/default/lib64' '-L/opt/cray/pe/mpt/7.7.6/gni/mpich-gnu/8.2/lib' '-L/opt/cray/rca/2.2.20-7.0.0.1_4.34__g8e3fb5b.ari/lib64' '-L/opt/cray/alps/6.6.50-7.0.0.1_3.35__g962f7108.ari/lib64' '-L/opt/cray/xpmem/2.2.17-7.0.0.1_3.24__g7acee3a.ari/lib64' '-L/opt/cray/pe/pmi/5.0.14/lib64' '-L/opt/cray/ugni/6.0.14.0-7.0.0.1_7.30__ge78e5b0.ari/lib64' '-L/opt/cray/udreg/2.3.2-7.0.0.1_4.27__g8175d3d.ari/lib64' '-L/opt/cray/pe/atp/2.1.3/libApp' '-L/opt/cray/wlm_detect/1.3.3-7.0.0.1_3.20__g7109084.ari/lib64'
as -v -I /opt/cray/pe/libsci/19.02.1/GNU/8.1/x86_64/include -I /opt/cray/pe/mpt/7.7.6/gni/mpich-gnu/8.2/include -I /opt/cray/rca/2.2.20-7.0.0.1_4.34__g8e3fb5b.ari/include -I /opt/cray/alps/6.6.50-7.0.0.1_3.35__g962f7108.ari/include -I /opt/cray/xpmem/2.2.17-7.0.0.1_3.24__g7acee3a.ari/include -I /opt/cray/gni-headers/5.0.12.0-7.0.0.1_7.39__g3b1768f.ari/include -I /opt/cray/pe/pmi/5.0.14/include -I /opt/cray/ugni/6.0.14.0-7.0.0.1_7.30__ge78e5b0.ari/include -I /opt/cray/udreg/2.3.2-7.0.0.1_4.27__g8175d3d.ari/include -I /opt/cray/wlm_detect/1.3.3-7.0.0.1_3.20__g7109084.ari/include -I /opt/cray/krca/2.2.5-7.0.0.1_4.34__g92086a7.ari/include -I /opt/cray-hss-devel/9.0.0/include --64 -o /tmp/ccg3Klvj.o /tmp/ccwl9GA7.s
GNU assembler version 2.31.1 (x86_64-suse-linux) using BFD version (GNU Binutils; SUSE Linux Enterprise 15) 2.31.1.20180828-6.3
COMPILER_PATH=/opt/gcc/8.2.0/snos/libexec/gcc/x86_64-suse-linux/8.2.0/:/opt/gcc/8.2.0/snos/libexec/gcc/x86_64-suse-linux/8.2.0/:/opt/gcc/8.2.0/snos/libexec/gcc/x86_64-suse-linux/:/opt/gcc/8.2.0/snos/lib/gcc/x86_64-suse-linux/8.2.0/:/opt/gcc/8.2.0/snos/lib/gcc/x86_64-suse-linux/
LIBRARY_PATH=/opt/gcc/8.2.0/snos/lib/gcc/x86_64-suse-linux/8.2.0/:/opt/gcc/8.2.0/snos/lib/gcc/x86_64-suse-linux/8.2.0/../../../../lib64/:/lib/../lib64/:/usr/lib/../lib64/:/opt/gcc/8.2.0/snos/lib/gcc/x86_64-suse-linux/8.2.0/../../../:/lib/:/usr/lib/
COLLECT_GCC_OPTIONS='-march=core-avx2' '-static' '-D' '__CRAYXC' '-D' '__CRAY_HASWELL' '-D' '__CRAYXT_COMPUTE_LINUX_TARGET' '-u' 'pthread_mutex_destroy' '-D' '__TARGET_LINUX__' '-v' '-I' '/opt/cray/pe/libsci/19.02.1/GNU/8.1/x86_64/include' '-I' '/opt/cray/pe/mpt/7.7.6/gni/mpich-gnu/8.2/include' '-I' '/opt/cray/rca/2.2.20-7.0.0.1_4.34__g8e3fb5b.ari/include' '-I' '/opt/cray/alps/6.6.50-7.0.0.1_3.35__g962f7108.ari/include' '-I' '/opt/cray/xpmem/2.2.17-7.0.0.1_3.24__g7acee3a.ari/include' '-I' '/opt/cray/gni-headers/5.0.12.0-7.0.0.1_7.39__g3b1768f.ari/include' '-I' '/opt/cray/pe/pmi/5.0.14/include' '-I' '/opt/cray/ugni/6.0.14.0-7.0.0.1_7.30__ge78e5b0.ari/include' '-I' '/opt/cray/udreg/2.3.2-7.0.0.1_4.27__g8175d3d.ari/include' '-I' '/opt/cray/wlm_detect/1.3.3-7.0.0.1_3.20__g7109084.ari/include' '-I' '/opt/cray/krca/2.2.5-7.0.0.1_4.34__g92086a7.ari/include' '-I' '/opt/cray-hss-devel/9.0.0/include' '-L/opt/cray/pe/libsci/19.02.1/GNU/8.1/x86_64/lib' '-L/opt/cray/dmapp/default/lib64' '-L/opt/cray/pe/mpt/7.7.6/gni/mpich-gnu/8.2/lib' '-L/opt/cray/rca/2.2.20-7.0.0.1_4.34__g8e3fb5b.ari/lib64' '-L/opt/cray/alps/6.6.50-7.0.0.1_3.35__g962f7108.ari/lib64' '-L/opt/cray/xpmem/2.2.17-7.0.0.1_3.24__g7acee3a.ari/lib64' '-L/opt/cray/pe/pmi/5.0.14/lib64' '-L/opt/cray/ugni/6.0.14.0-7.0.0.1_7.30__ge78e5b0.ari/lib64' '-L/opt/cray/udreg/2.3.2-7.0.0.1_4.27__g8175d3d.ari/lib64' '-L/opt/cray/pe/atp/2.1.3/libApp' '-L/opt/cray/wlm_detect/1.3.3-7.0.0.1_3.20__g7109084.ari/lib64'
/opt/gcc/8.2.0/snos/libexec/gcc/x86_64-suse-linux/8.2.0/collect2 -plugin /opt/gcc/8.2.0/snos/libexec/gcc/x86_64-suse-linux/8.2.0/liblto_plugin.so -plugin-opt=/opt/gcc/8.2.0/snos/libexec/gcc/x86_64-suse-linux/8.2.0/lto-wrapper -plugin-opt=-fresolution=/tmp/ccCWTErv.res -plugin-opt=-pass-through=-lgcc -plugin-opt=-pass-through=-lgcc_eh -plugin-opt=-pass-through=-lc -m elf_x86_64 -static -u pthread_mutex_destroy /usr/lib/../lib64/crt1.o /usr/lib/../lib64/crti.o /opt/gcc/8.2.0/snos/lib/gcc/x86_64-suse-linux/8.2.0/crtbeginT.o -L/opt/cray/pe/libsci/19.02.1/GNU/8.1/x86_64/lib -L/opt/cray/dmapp/default/lib64 -L/opt/cray/pe/mpt/7.7.6/gni/mpich-gnu/8.2/lib -L/opt/cray/rca/2.2.20-7.0.0.1_4.34__g8e3fb5b.ari/lib64 -L/opt/cray/alps/6.6.50-7.0.0.1_3.35__g962f7108.ari/lib64 -L/opt/cray/xpmem/2.2.17-7.0.0.1_3.24__g7acee3a.ari/lib64 -L/opt/cray/pe/pmi/5.0.14/lib64 -L/opt/cray/ugni/6.0.14.0-7.0.0.1_7.30__ge78e5b0.ari/lib64 -L/opt/cray/udreg/2.3.2-7.0.0.1_4.27__g8175d3d.ari/lib64 -L/opt/cray/pe/atp/2.1.3/libApp -L/opt/cray/wlm_detect/1.3.3-7.0.0.1_3.20__g7109084.ari/lib64 -L/opt/gcc/8.2.0/snos/lib/gcc/x86_64-suse-linux/8.2.0 -L/opt/gcc/8.2.0/snos/lib/gcc/x86_64-suse-linux/8.2.0/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/opt/gcc/8.2.0/snos/lib/gcc/x86_64-suse-linux/8.2.0/../../.. /tmp/ccg3Klvj.o -latomic -rpath=/opt/cray/pe/gcc-libs --no-as-needed -lAtpSigHandler -lAtpSigHCommData --undefined=_ATP_Data_Globals --undefined=__atpHandlerInstall -lpthread -Ttext-segment=0x20000000 -zmax-page-size=0x20000000 --whole-archive -lhugetlbfs --no-whole-archive -lsci_gnu_82_mpi -lsci_gnu_82 -lpthread -lhugetlbfs -lmpich_gnu_82 -lrt -lugni -lpthread -lpmi -lpthread -lalpslli -lpthread -lwlm_detect -lalpsutil -lpthread -lrca -lxpmem -lugni -lpthread -ludreg --as-needed -lgfortran -lquadmath --no-as-needed --as-needed -lmvec --no-as-needed --as-needed -lm --no-as-needed --as-needed -lpthread --no-as-needed --start-group -lgcc -lgcc_eh -lc --end-group /opt/gcc/8.2.0/snos/lib/gcc/x86_64-suse-linux/8.2.0/crtend.o /usr/lib/../lib64/crtn.o
COLLECT_GCC_OPTIONS='-march=core-avx2' '-static' '-D' '__CRAYXC' '-D' '__CRAY_HASWELL' '-D' '__CRAYXT_COMPUTE_LINUX_TARGET' '-u' 'pthread_mutex_destroy' '-D' '__TARGET_LINUX__' '-v' '-I' '/opt/cray/pe/libsci/19.02.1/GNU/8.1/x86_64/include' '-I' '/opt/cray/pe/mpt/7.7.6/gni/mpich-gnu/8.2/include' '-I' '/opt/cray/rca/2.2.20-7.0.0.1_4.34__g8e3fb5b.ari/include' '-I' '/opt/cray/alps/6.6.50-7.0.0.1_3.35__g962f7108.ari/include' '-I' '/opt/cray/xpmem/2.2.17-7.0.0.1_3.24__g7acee3a.ari/include' '-I' '/opt/cray/gni-headers/5.0.12.0-7.0.0.1_7.39__g3b1768f.ari/include' '-I' '/opt/cray/pe/pmi/5.0.14/include' '-I' '/opt/cray/ugni/6.0.14.0-7.0.0.1_7.30__ge78e5b0.ari/include' '-I' '/opt/cray/udreg/2.3.2-7.0.0.1_4.27__g8175d3d.ari/include' '-I' '/opt/cray/wlm_detect/1.3.3-7.0.0.1_3.20__g7109084.ari/include' '-I' '/opt/cray/krca/2.2.5-7.0.0.1_4.34__g92086a7.ari/include' '-I' '/opt/cray-hss-devel/9.0.0/include' '-L/opt/cray/pe/libsci/19.02.1/GNU/8.1/x86_64/lib' '-L/opt/cray/dmapp/default/lib64' '-L/opt/cray/pe/mpt/7.7.6/gni/mpich-gnu/8.2/lib' '-L/opt/cray/rca/2.2.20-7.0.0.1_4.34__g8e3fb5b.ari/lib64' '-L/opt/cray/alps/6.6.50-7.0.0.1_3.35__g962f7108.ari/lib64' '-L/opt/cray/xpmem/2.2.17-7.0.0.1_3.24__g7acee3a.ari/lib64' '-L/opt/cray/pe/pmi/5.0.14/lib64' '-L/opt/cray/ugni/6.0.14.0-7.0.0.1_7.30__ge78e5b0.ari/lib64' '-L/opt/cray/udreg/2.3.2-7.0.0.1_4.27__g8175d3d.ari/lib64' '-L/opt/cray/pe/atp/2.1.3/libApp' '-L/opt/cray/wlm_detect/1.3.3-7.0.0.1_3.20__g7109084.ari/lib64'
pdavis@cori02:~/tests>
```
My cmake line is `cmake .. -DCMAKE_C_COMPILER=cc -DCMAKE_Fortran_COMPILER=ftn -DCMAKE_CXX_COMPILER=CC`, and my modules are:
```
1) modules/3.2.11.1 13) pmi/5.0.14
2) nsg/1.2.0 14) dmapp/7.1.1-7.0.0.1_5.20__g25e5077.ari
3) gcc/8.2.0 15) gni-headers/5.0.12.0-7.0.0.1_7.39__g3b1768f.ari
4) craype-haswell 16) xpmem/2.2.17-7.0.0.1_3.24__g7acee3a.ari
5) craype-hugepages2M 17) job/2.2.4-7.0.0.1_3.30__g36b56f4.ari
6) craype-network-aries 18) dvs/2.11_2.2.137-7.0.0.1_10.1__g04d35b33
7) craype/2.5.18 19) alps/6.6.50-7.0.0.1_3.35__g962f7108.ari
8) cray-mpich/7.7.6 20) rca/2.2.20-7.0.0.1_4.34__g8e3fb5b.ari
9) altd/2.0 21) atp/2.1.3
10) cray-libsci/19.02.1 22) PrgEnv-gnu/6.0.5
11) udreg/2.3.2-7.0.0.1_4.27__g8175d3d.ari 23) cmake/3.14.4
12) ugni/6.0.14.0-7.0.0.1_7.30__ge78e5b0.ari
```
As a possibly unrelated aside, I had a terrible time getting libtool to statically link libatomic on Cori when building libfabric. I had to do `make LDFLAGS=-all-static` to force static linking, despite configuring libfabric with `--enable-static --disable-shared`. It seems like this is a known feature of libtool in certain circumstances.
I can work around this by editing CMakeCache.txt to insert the absolute path of libatomic, and I can successfully build. Something is clearly wrong somewhere, but I'm not sure what I've done wrong.
2.5.0 Production Releasehttps://code.ornl.gov/pnb/ADIOS2/-/issues/1534Segmentation fault when setting MPI transportation method2019-09-03T18:10:33ZPodhorszki, NorbertSegmentation fault when setting MPI transportation method*Created by: khou2020*
I got segmentation fault calling adios2_open if i set transportation library tpo MPI.
Anyone klnow what happened?
`
ad = adios2_init(MPI_COMM_WORLD, adios2_debug_mode_off);
io = adios2_declare...*Created by: khou2020*
I got segmentation fault calling adios2_open if i set transportation library tpo MPI.
Anyone klnow what happened?
`
ad = adios2_init(MPI_COMM_WORLD, adios2_debug_mode_off);
io = adios2_declare_io(ad, "subarray");
err = adios2_set_engine(io, "BPFile");
err = adios2_add_transport(&tid, io, "File");
err = adios2_set_transport_parameter(io, tid, "Library", "MPI");
eng = adios2_open(io, fname, adios2_mode_write); // => Segmentation fault
`